Gaggle Genome Browser Web (GGBWeb) is a web tool that enables interactive visualization of systems-scale data in the context of the genome. GGBWeb implements a suite of features for large-scale data exploration within an easy-to-embed, browser-independent web application. The application is open-source, highly-customizable and easily-integrated into existing HTML5 web applications. Multiple data types can be imported, rendered, paired, and synchronously animated by GGBWeb, including: heat maps, line charts and a novel positional quantitative-string track.